Detection of insulin oligomeric forms by a novel surface plasmon resonance ‐diffusion coefficient based approach
AbstractInsulin is commonly used to treat diabetes and undergoes aggregation at the site of repeated injections in diabetic patients. Moreover, aggregation is also observed during its industrial production and transport and should be avoided to preserve its bioavailability to correctly adjust glucose levels in diabetic patients. However, monitoring the effect of various parameters (pH, protein concentration, metal ions, etc.) on the insulin aggregation and oligomerization state is very challenging. In this work, we have applied a novel Surface Plasmon Resonance (SPR)-based experimental approach to insulin solutions at vari...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Damiano Calcagno,
Maria Luisa Perina,
Gabriele Antonio Zingale,
Irene Pandino,
Nunzio Tuccitto,
Valentina Oliveri,
Maria Cristina Parravano,
Giuseppe Grasso Tags: RESEARCH ARTICLE Source Type: research
Structural dynamics and functional cooperativity of human NQO1 by ambient temperature serial crystallography and simulations
AbstractThe human NQO1 (hNQO1) is a flavin adenine nucleotide (FAD)-dependent oxidoreductase that catalyzes the two-electron reduction of quinones to hydroquinones, being essential for the antioxidant defense system, stabilization of tumor suppressors, and activation of quinone-based chemotherapeutics. Moreover, it is overexpressed in several tumors, which makes it an attractive cancer drug target. To decipher new structural insights into the flavin reductive half-reaction of the catalytic mechanism of hNQO1, we have carried serial crystallography experiments at new ID29 beamline of the ESRF to determine, to the best of ou...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Alice Grieco,
Sergio Boneta,
Jos é A. Gavira,
Angel L. Pey,
Shibom Basu,
Julien Orlans,
Daniele de Sanctis,
Milagros Medina,
Jose Manuel Martin‐Garcia Tags: RESEARCH ARTICLE Source Type: research
Ca2+/CaM dependent protein kinase II (CaMKII) α and CaMKIIβ hub domains adopt distinct oligomeric states and stabilities
AbstractCa2+/calmodulin-dependent protein kinase II (CaMKII) is a multidomain serine/threonine kinase that plays important roles in the brain, heart, muscle tissue, and eggs/sperm. The N-terminal kinase and regulatory domain is connected by a flexible linker to the C-terminal hub domain. The hub domain drives the oligomeric organization of CaMKII, assembling the kinase domains into high local concentration. Previous structural studies have shown multiple stoichiometries of the holoenzyme as well as the hub domain alone. Here, we report a comprehensive study of the hub domain stoichiometry and stability in solution. We solv...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Can Özden,
Sara MacManus,
Ruth Adafia,
Alfred Samkutty,
Ana P. Torres‐Ocampo,
Scott C. Garman,
Margaret M. Stratton Tags: RESEARCH ARTICLE Source Type: research
Reengineering of a flavin ‐binding fluorescent protein using ProteinMPNN
AbstractRecent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non-proteinaceous ligand-binding protein, flavin-based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acid...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Andrey Nikolaev,
Alexander Kuzmin,
Elena Markeeva,
Elizaveta Kuznetsova,
Yury L. Ryzhykau,
Oleg Semenov,
Arina Anuchina,
Alina Remeeva,
Ivan Gushchin Tags: RESEARCH NOTE Source Type: research
Examining evolutionary scale modeling ‐derived different‐dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow
AbstractMolecular features play an important role in different bio-chem-informatics tasks, such as the Quantitative Structure –Activity Relationships (QSAR) modeling. Several pre-trained models have been recently created to be used in downstream tasks, either by fine-tuning a specific model or by extracting features to feed traditional classifiers. In this regard, a new family of Evolutionary Scale Modeling models (terme d as ESM-2 models) was recently introduced, demonstrating outstanding results in protein structure prediction benchmarks. Herein, we studied the usefulness of the different-dimensional embeddings derived...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Karla L. Mart ínez‐Mauricio,
César R. García‐Jacas,
Greneter Cordoves‐Delgado Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins
AbstractStructure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II lo...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Qian Wang,
Christopher DiForte,
Aleksey Aleshintsev,
Gianna Elci,
Shibani Bhattacharya,
Angelo Bongiorno,
Rupal Gupta Tags: RESEARCH ARTICLE Source Type: research
Construction of a versatile fusion protein for targeted therapy and immunotherapy
In this study, we expanded the application of antibodies (Abs) by constructing a fusion protein as a versatile tool for Ab-based target cell detection, delivery, and therapy. We first constructed a SpaC Catcher (SpaCC for short) fusion protein that included the C domains of Staphylococcal protein A (SpaC) and the SpyCatcher. SpaCC conjugated with SpyTag-X (S-X) to form the SpaCC-S-X complex, which binds non-covalently to an Ab to form the Ab-SpaCC-S-X protein complex. The “X” can be a variety of small molecules such as fluoresceins, cell-penetrating peptide TAT, Monomethyl auristatin E (MMAE), and DNA. We found that Ab...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Xiu ‐Song Huang,
Li‐Ting Yang,
Ke Yang,
Hang Zhou,
Tuersunayi Abudureheman,
Wei‐Wei Zheng,
Kai‐Ming Chen,
Cai‐Wen Duan Tags: RESEARCH ARTICLE Source Type: research
Engineering of IF1 ‐susceptive bacterial F1‐ATPase
AbstractIF1, an inhibitor protein of mitochondrial ATP synthase, suppresses ATP hydrolytic activity of F1. One of the unique features of IF1 is the selective inhibition in mitochondrial F1 (MF1); it inhibits catalysis of MF1 but does not affect F1 with bacterial origin despite high sequence homology between MF1 and bacterial F1. Here, we aimed to engineer thermophilicBacillus F1 (TF1) to confer the susceptibility to IF1 for elucidating the molecular mechanism of selective inhibition of IF1. We first examined the IF1-susceptibility of hybrid F1s, composed of each subunit originating frombovine MF1 (bMF1) or TF1. It was clea...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Yuichiro C. Hatasaki,
Ryohei Kobayashi,
Ryo R. Watanabe,
Mayu Hara,
Hiroshi Ueno,
Hiroyuki Noji Tags: RESEARCH ARTICLE Source Type: research
Identification of a novel DNA repair inhibitor using an in silico driven approach shows effective combinatorial activity with genotoxic agents against multidrug‐resistant Escherichia coli
This study offers a novel approach for the potential development of new compounds for use as adjuvants in antineoplastic therapy. (Source: Protein Science)
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Lorenzo Bernacchia,
Antoine Paris,
Arya Gupta,
Robert J. Charman,
Jake McGreig,
Mark N. Wass,
Neil M. Kad Tags: RESEARCH ARTICLE Source Type: research
Unraveling the underlying mechanisms of reduced amyloidogenic properties in human calcitonin via double mutations
This study delves into the oligomerization and helical structure formation of the hCT double mutant (Y12LN17H hCT, noted as DM hCT), as well as two single mutants (Y12L and N17H), aiming to elucidate the mechanism behind hCT fibrillization. In addition, computational prediction tools were employed again to identify potential substitutes. Although the results yielded were not entirely satisfactory, a comparison between the newly examined and previously found hCT double mutants provides insights into the reduced aggregation propensity of the latter. This research endeavor holds the promise of informing the design of more eff...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Yu ‐Pei Chang,
Pei‐Chun Pan,
Ling‐Hsien Tu Tags: RESEARCH ARTICLE Source Type: research
Adaptable SEC ‐SAXS data collection for higher quality structure analysis in solution
AbstractThe two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4 –2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enab...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Tsutomu Matsui,
Ivan Rajkovic,
Blaine H. M. Mooers,
Ping Liu,
Thomas M. Weiss Tags: TOOLS FOR PROTEIN SCIENCE Source Type: research
A cellulosomal double ‐dockerin module from Clostridium thermocellum shows distinct structural and cohesin‐binding features
In this study, we characterized the structure and mode of assembly of a tandem bimodular double-dockerin, which is connected to a putative S8 protease in the cellulosome-producing bacterium,Clostridium thermocellum. Crystal and NMR structures of the double-dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double-dockerin displays a preference for binding to the cell-wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual-binding mode, while the second...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Chao Chen,
Hongwu Yang,
Sheng Dong,
Cai You,
Sarah Mora ïs,
Edward A. Bayer,
Ya‐Jun Liu,
Jinsong Xuan,
Qiu Cui,
Itzhak Mizrahi,
Yingang Feng Tags: RESEARCH ARTICLE Source Type: research
The structural landscape of the immunoglobulin fold by large ‐scale de novo design
AbstractDe novo designing immunoglobulin-like frameworks that allow for functional loop diversification shows great potential for crafting antibody-like scaffolds with fully customizable structures and functions. In this work, we combined de novo parametric design with deep-learning methods for protein structure prediction and design to explore the structural landscape of 7-stranded immunoglobulin domains. After screening folding of nearly 4 million designs, we have assembled a structurally diverse library of ~50,000 immunoglobulin domains with high-confidence AlphaFold2 predictions and structures diverging from naturally ...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Jorge Roel ‐Touris,
Lourdes Carcelén,
Enrique Marcos Tags: RESEARCH ARTICLE Source Type: research
Labile assembly of a tardigrade protein induces biostasis
AbstractTardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: S. Sanchez ‐Martinez,
K. Nguyen,
S. Biswas,
V. Nicholson,
A. V. Romanyuk,
J. Ramirez,
S. Kc,
A. Akter,
C. Childs,
E. K. Meese,
E. T. Usher,
G. M. Ginell,
F. Yu,
E. Gollub,
M. Malferrari,
F. Francia,
G. Venturoli,
E. W. Martin,
F. Capor Tags: RESEARCH ARTICLE Source Type: research
Assessing the mechanism of fast ‐cycling cancer‐associated mutations of Rac1 small Rho GTPase
AbstractRho-GTPases proteins function as molecular switches alternating from an active to an inactive state upon Guanosine triphosphate (GTP) binding and hydrolysis to Guanosine diphosphate (GDP). Among them, Rac subfamily regulates cell dynamics, being overexpressed in distinct cancer types. Notably, these proteins are object of frequent cancer-associated mutations at Pro29 (P29S, P29L, and P29Q). To assess the impact of these mutations on Rac1 structure and function, we performed extensive all-atom molecular dynamics simulations on wild-type (wt) and oncogenic isoforms of this protein in GDP- and GTP-bound states. Our re...
Source: Protein Science - March 19, 2024 Category: Biochemistry Authors: Angela Parise,
Alessandra Magistrato Tags: RESEARCH ARTICLE Source Type: research
